[ccp4bb] Coot's hidden talents!
Hi Just noticed this - http://www.bbc.co.uk/news/uk-20978904 do we know the artist? He has just moved to Cambridge... Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] Symmetry operator
I am afraid now I just use PISA at the EBI to answer this sort of question . It tells you the answer with lots of other useful information as well, and then you can use your intelligence to see why that operator is the correct one! Eleanor On 11 Jan 2013, at 01:05, James Stroud wrote: The transformation matrix describing the symmetry is sensitive to the coordinate system origin. You should center the entire tetramer on the origin (0, 0, 0), where the origin coincides with the point symmetry element. If you have a tetramer with true point symmetry, then the center of the tetramer should be the center of mass. Then you can use lsq-expl from O or whatever the equivalent is in pymol, phenix, or coot to get the transformation matrix between any two monomers. Repeated application of that transformation matrix to any monomer of the tetramer should generate the tetramer. James On Jan 10, 2013, at 5:48 PM, james09 pruza wrote: Hi, Which program outputs the symmetry operator (rotation and translation)? I have a dimer in the asymmetric unit and need to know the symmetry operator to get a tetramer, the active molecule. James
[ccp4bb] EMBO practical course on Computational Structural Biology - from data to structure to function, EMBL Hamburg, 15-19 April 2013
Dear colleagues, We are pleased to announce the upcoming EMBO practical course on Computational Structural Biology - from data to structure to function EMBL Hamburg, Germany 15th - 19th April 2013 The course covers computational aspects of protein structure determination, validation and analysis, including background in X-ray crystallography, Nuclear Magnetic Resonance Spectroscopy, Electron Microscopy and Small-angle X-ray scattering and hands-on experience in model building from X-ray diffraction data, comparing and integrating different types of structural data, and the differences in interpretation. Students will also learn to critically examine and validate data from these techniques. The course is aimed at PhD students and post-docs working on the collection and analysis of protein structure data. The goal is to provide them with insight into the protein structure determination process, how to critically assess the quality of data from models, and to provide expertise in the integration and visualisation of data from different techniques, thus allowing the analysis of protein structure data for functional relationships. For more information and to apply, please go to: http://events.embo.org/13-comp-structure/ Application deadline: 15th February 2013 We look forward to receiving your application! Kind regards, Margret On behalf of the organising committee, Gerard Kleywegt Victor Lamzin Christine Orengo Gert Vriend Rosemary Wilson
Re: [ccp4bb] Coot's hidden talents!
if you zoom in 10exp9-10exp10 times (lots of cmd-+ in macosx), you can see the amino acids. tried to check the accuracy; however, I couldn't find the mtz file to display the density...does this journal not enforce depositing the data? Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 11 Jan 2013, at 11:47, Harry Powell wrote: Hi Just noticed this - http://www.bbc.co.uk/news/uk-20978904 do we know the artist? He has just moved to Cambridge... Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] Coot's hidden talents!
To be honest I preferred this more homespun work: http://www.guardian.co.uk/science/gallery/2013/jan/10/research-as-art-competition-in-pictures?INTCMP=SRCH#/?picture=402066318index=3 Somewhat reminiscent of Byron's Bender models: http://www.umass.edu/microbio/rasmol/history.htm#bender /Derek On 11 Jan 2013, at 13:08, Mark J van Raaij mjvanra...@cnb.csic.es wrote: if you zoom in 10exp9-10exp10 times (lots of cmd-+ in macosx), you can see the amino acids. tried to check the accuracy; however, I couldn't find the mtz file to display the density...does this journal not enforce depositing the data? Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 11 Jan 2013, at 11:47, Harry Powell wrote: Hi Just noticed this - http://www.bbc.co.uk/news/uk-20978904 do we know the artist? He has just moved to Cambridge... Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] Coot's hidden talents!
Friday afternoon Good time to look at some artistic representations of protein molecules. This is pretty amazing: http://www.julianvossandreae.com/ Johan On 11 January 2013 14:26, Derek Logan derek.lo...@biochemistry.lu.se wrote: To be honest I preferred this more homespun work: http://www.guardian.co.uk/science/gallery/2013/jan/10/research-as-art-competition-in-pictures?INTCMP=SRCH#/?picture=402066318index=3 Somewhat reminiscent of Byron's Bender models: http://www.umass.edu/microbio/rasmol/history.htm#bender /Derek On 11 Jan 2013, at 13:08, Mark J van Raaij mjvanra...@cnb.csic.es wrote: if you zoom in 10exp9-10exp10 times (lots of cmd-+ in macosx), you can see the amino acids. tried to check the accuracy; however, I couldn't find the mtz file to display the density...does this journal not enforce depositing the data? Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 11 Jan 2013, at 11:47, Harry Powell wrote: Hi Just noticed this - http://www.bbc.co.uk/news/uk-20978904 do we know the artist? He has just moved to Cambridge... Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) -- Dr. Johan P. Turkenburg X-ray facilities manager York Structural Biology Laboratory University of York Phone (+) 44 1904 328251 York YO10 5DD UK Fax (+) 44 1904 328266 Note new email address johan.turkenb...@york.ac.uk
Re: [ccp4bb] Coot's hidden talents!
Surprised Mercedes didn't sued him for that :-) @Mr. Emsley I assume you soon will be Sir Emsley after that marvelous painting.mentioned in Harry's email. Jürgen .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Jan 11, 2013, at 10:21 AM, Johan Turkenburg wrote: Friday afternoon Good time to look at some artistic representations of protein molecules. This is pretty amazing: http://www.julianvossandreae.com/ Johan On 11 January 2013 14:26, Derek Logan derek.lo...@biochemistry.lu.se wrote: To be honest I preferred this more homespun work: http://www.guardian.co.uk/science/gallery/2013/jan/10/research-as-art-competition-in-pictures?INTCMP=SRCH#/?picture=402066318index=3 Somewhat reminiscent of Byron's Bender models: http://www.umass.edu/microbio/rasmol/history.htm#bender /Derek On 11 Jan 2013, at 13:08, Mark J van Raaij mjvanra...@cnb.csic.es wrote: if you zoom in 10exp9-10exp10 times (lots of cmd-+ in macosx), you can see the amino acids. tried to check the accuracy; however, I couldn't find the mtz file to display the density...does this journal not enforce depositing the data? Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 11 Jan 2013, at 11:47, Harry Powell wrote: Hi Just noticed this - http://www.bbc.co.uk/news/uk-20978904 do we know the artist? He has just moved to Cambridge... Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) -- Dr. Johan P. Turkenburg X-ray facilities manager York Structural Biology Laboratory University of York Phone (+) 44 1904 328251 York YO10 5DD UK Fax (+) 44 1904 328266 Note new email address johan.turkenb...@york.ac.uk
Re: [ccp4bb] Convert cbf to png/tiff?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Pat, for several versions adxv has been able to save as tif, although (maybe) not from the GUI. If you type 'adxv -?' you get the instruction manual including the '-sa' option which converts to some tiff file. Buy the whey, tiff is not an image format, it is an 'image file format' and does not per se guarantuee a losless image, e.g. TIFF allows to contain a lossy jpeg image. Cheers, Tim On 01/10/2013 09:45 PM, Patrick Loll wrote: adxv reads cbf images, and can save them as postscript (actually, it's supposed to be able to save the image as tiff as well, but at least on my version of the program that feature doesn't work). Pat On 10 Jan 2013, at 3:36 PM, Frank von Delft wrote: Hello all - anybody know an easy way to convert CBF images (Pilatus) into something lossless like tiff or png? Ideally *easy* as in r e a l l y e a s y and not requiring extensive installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQ8D3qUxlJ7aRr7hoRAk72AJ9oATvw/cMviZuUNS0XhkKoZMrLKwCgwqKA 6v1VeBG4GGtUJTwL7w365Ds= =u7hG -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: Re: [ccp4bb] Convert cbf to png/tiff?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Nat! How recent is recent? From today's 'phenix-online.org': New Phenix version 1.8.1 now available, but tg@slartibartfast:~/uni/datasets/nk/xds_run3$ labelit.png_1.8.1-1168 DX-CORRECTIONS.cbf Traceback (most recent call last): File /xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py, line 27, in module OV = overlay_plain(infile,graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py, line 6, in __init__ OverlayDriverClass.__init__(self,infile,graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/overlay_distl.py, line 19, in __init__ self.I = GenericImageWorker(infile,binning=graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/graphics/support.py, line 12, in __init__ images = ImageFiles(imagenames,labelit_commands) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py, line 184, in __init__ self.filenames = FileNames(arg_module,phil_params) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py, line 70, in __init__ self.interface3_parse_command() File /xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py, line 138, in interface3_parse_command self.interface3_FN_factory(os.path.abspath(file),error_message=File name not accepted) File /xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py, line 127, in interface3_FN_factory raise Exception(Input error: +error_message) Exception: Input error: File name not accepted Compared to: tg@slartibartfast:~/uni/datasets/nk/xds_run3$ adxv -sa DX-CORRECTIONS.cbf DX-CORRECTIONS.tiff Adxv Version 1.9.8 Copyright (C) 1994-2011 by Andrew Arvai, Area Detector Systems Corporation Recognized CBF format data. Warning: Could not find diffrn_frame_data or diffrn_data_frame tg@slartibartfast:~/uni/datasets/nk/xds_run3$ identify DX-CORRECTIONS.tiff DX-CORRECTIONS.tiff TIFF 768x768 768x768+0+0 8-bit PseudoClass 256c 592KB 0.000u 0:00.000 Cheers, Tim On 01/10/2013 09:59 PM, Frank von Delft wrote: Brilliant - thanks Nat!! Easy to work around that feature. And thanks Nick!! Original Message Subject: Re: [ccp4bb] Convert cbf to png/tiff? Date: Thu, 10 Jan 2013 12:47:21 -0800 From: Nat Echols nathaniel.ech...@gmail.com To: Frank von Delft frank.vonde...@sgc.ox.ac.uk Using any recent Phenix distribution: labelit.png file_name For reasons unknown to me, the output is named plain.png - I will bug Nick about this. On Thu, Jan 10, 2013 at 12:36 PM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: Hello all - anybody know an easy way to convert CBF images (Pilatus) into something lossless like tiff or png? Ideally *easy* as in r e a l l y e a s y and not requiring extensive installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQ8D8kUxlJ7aRr7hoRAkcsAJ9Z4JmZ3zAvFYDRMaGbzunMYTjLNACfQWBP s3YM17LqF9zvCsAK8ezG8xQ= =hXlq -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: Re: [ccp4bb] Convert cbf to png/tiff?
I got that error blurb too when I run without an image on the commandline. Not very elegant. Try: labelit.png --help On 11/01/2013 16:34, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Nat! How recent is recent? From today's 'phenix-online.org': New Phenix version 1.8.1 now available, but tg@slartibartfast:~/uni/datasets/nk/xds_run3$ labelit.png_1.8.1-1168 DX-CORRECTIONS.cbf Traceback (most recent call last): File /xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py, line 27, in module OV = overlay_plain(infile,graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py, line 6, in __init__ OverlayDriverClass.__init__(self,infile,graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/overlay_distl.py, line 19, in __init__ self.I = GenericImageWorker(infile,binning=graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/graphics/support.py, line 12, in __init__ images = ImageFiles(imagenames,labelit_commands) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py, line 184, in __init__ self.filenames = FileNames(arg_module,phil_params) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py, line 70, in __init__ self.interface3_parse_command() File /xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py, line 138, in interface3_parse_command self.interface3_FN_factory(os.path.abspath(file),error_message=File name not accepted) File /xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py, line 127, in interface3_FN_factory raise Exception(Input error: +error_message) Exception: Input error: File name not accepted Compared to: tg@slartibartfast:~/uni/datasets/nk/xds_run3$ adxv -sa DX-CORRECTIONS.cbf DX-CORRECTIONS.tiff Adxv Version 1.9.8 Copyright (C) 1994-2011 by Andrew Arvai, Area Detector Systems Corporation Recognized CBF format data. Warning: Could not find diffrn_frame_data or diffrn_data_frame tg@slartibartfast:~/uni/datasets/nk/xds_run3$ identify DX-CORRECTIONS.tiff DX-CORRECTIONS.tiff TIFF 768x768 768x768+0+0 8-bit PseudoClass 256c 592KB 0.000u 0:00.000 Cheers, Tim On 01/10/2013 09:59 PM, Frank von Delft wrote: Brilliant - thanks Nat!! Easy to work around that feature. And thanks Nick!! Original Message Subject: Re: [ccp4bb] Convert cbf to png/tiff? Date: Thu, 10 Jan 2013 12:47:21 -0800 From: Nat Echols nathaniel.ech...@gmail.com To: Frank von Delft frank.vonde...@sgc.ox.ac.uk Using any recent Phenix distribution: labelit.png file_name For reasons unknown to me, the output is named plain.png - I will bug Nick about this. On Thu, Jan 10, 2013 at 12:36 PM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: Hello all - anybody know an easy way to convert CBF images (Pilatus) into something lossless like tiff or png? Ideally *easy* as in r e a l l y e a s y and not requiring extensive installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQ8D8kUxlJ7aRr7hoRAkcsAJ9Z4JmZ3zAvFYDRMaGbzunMYTjLNACfQWBP s3YM17LqF9zvCsAK8ezG8xQ= =hXlq -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: Re: [ccp4bb] Convert cbf to png/tiff?
I think the help message refers to another program. Anyway, it's an extremely simple script - having examined the code, the command-line invocation is: labelit.png input_file [output_file] and that's it - no other options available. But Nick or I will fix it so it prints something more useful if run without arguments. -Nat On Fri, Jan 11, 2013 at 9:33 AM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: I got that error blurb too when I run without an image on the commandline. Not very elegant. Try: labelit.png --help On 11/01/2013 16:34, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Nat! How recent is recent? From today's 'phenix-online.org': New Phenix version 1.8.1 now available, but tg@slartibartfast:~/uni/datasets/nk/xds_run3$ labelit.png_1.8.1-1168 DX-CORRECTIONS.cbf Traceback (most recent call last): File /xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py, line 27, in module OV = overlay_plain(infile,graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py, line 6, in __init__ OverlayDriverClass.__init__(self,infile,graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/overlay_distl.py, line 19, in __init__ self.I = GenericImageWorker(infile,binning=graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/graphics/support.py, line 12, in __init__ images = ImageFiles(imagenames,labelit_commands) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py, line 184, in __init__ self.filenames = FileNames(arg_module,phil_params) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py, line 70, in __init__ self.interface3_parse_command() File /xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py, line 138, in interface3_parse_command self.interface3_FN_factory(os.path.abspath(file),error_message=File name not accepted) File /xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py, line 127, in interface3_FN_factory raise Exception(Input error: +error_message) Exception: Input error: File name not accepted Compared to: tg@slartibartfast:~/uni/datasets/nk/xds_run3$ adxv -sa DX-CORRECTIONS.cbf DX-CORRECTIONS.tiff Adxv Version 1.9.8 Copyright (C) 1994-2011 by Andrew Arvai, Area Detector Systems Corporation Recognized CBF format data. Warning: Could not find diffrn_frame_data or diffrn_data_frame tg@slartibartfast:~/uni/datasets/nk/xds_run3$ identify DX-CORRECTIONS.tiff DX-CORRECTIONS.tiff TIFF 768x768 768x768+0+0 8-bit PseudoClass 256c 592KB 0.000u 0:00.000 Cheers, Tim On 01/10/2013 09:59 PM, Frank von Delft wrote: Brilliant - thanks Nat!! Easy to work around that feature. And thanks Nick!! Original Message Subject: Re: [ccp4bb] Convert cbf to png/tiff? Date: Thu, 10 Jan 2013 12:47:21 -0800 From: Nat Echols nathaniel.ech...@gmail.com To: Frank von Delft frank.vonde...@sgc.ox.ac.uk Using any recent Phenix distribution: labelit.png file_name For reasons unknown to me, the output is named plain.png - I will bug Nick about this. On Thu, Jan 10, 2013 at 12:36 PM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: Hello all - anybody know an easy way to convert CBF images (Pilatus) into something lossless like tiff or png? Ideally *easy* as in r e a l l y e a s y and not requiring extensive installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQ8D8kUxlJ7aRr7hoRAkcsAJ9Z4JmZ3zAvFYDRMaGbzunMYTjLNACfQWBP s3YM17LqF9zvCsAK8ezG8xQ= =hXlq -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: Re: [ccp4bb] Convert cbf to png/tiff?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The formatting of icedove probably created confusion, but these error message come from running labelit.png WITH the file DX-CORRECTIONS.cbf as one and only command line option and no output is created. adxv has not problem dealing with XDS cbf-files. Tim On 01/11/2013 06:43 PM, Nat Echols wrote: I think the help message refers to another program. Anyway, it's an extremely simple script - having examined the code, the command-line invocation is: labelit.png input_file [output_file] and that's it - no other options available. But Nick or I will fix it so it prints something more useful if run without arguments. -Nat On Fri, Jan 11, 2013 at 9:33 AM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: I got that error blurb too when I run without an image on the commandline. Not very elegant. Try: labelit.png --help On 11/01/2013 16:34, Tim Gruene wrote: Hi Nat! How recent is recent? From today's 'phenix-online.org': New Phenix version 1.8.1 now available, but tg@slartibartfast:~/uni/datasets/nk/xds_run3$ labelit.png_1.8.1-1168 DX-CORRECTIONS.cbf Traceback (most recent call last): File /xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py, line 27, in module OV = overlay_plain(infile,graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py, line 6, in __init__ OverlayDriverClass.__init__(self,infile,graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/overlay_distl.py, line 19, in __init__ self.I = GenericImageWorker(infile,binning=graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/graphics/support.py, line 12, in __init__ images = ImageFiles(imagenames,labelit_commands) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py, line 184, in __init__ self.filenames = FileNames(arg_module,phil_params) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py, line 70, in __init__ self.interface3_parse_command() File /xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py, line 138, in interface3_parse_command self.interface3_FN_factory(os.path.abspath(file),error_message=File name not accepted) File /xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py, line 127, in interface3_FN_factory raise Exception(Input error: +error_message) Exception: Input error: File name not accepted Compared to: tg@slartibartfast:~/uni/datasets/nk/xds_run3$ adxv -sa DX-CORRECTIONS.cbf DX-CORRECTIONS.tiff Adxv Version 1.9.8 Copyright (C) 1994-2011 by Andrew Arvai, Area Detector Systems Corporation Recognized CBF format data. Warning: Could not find diffrn_frame_data or diffrn_data_frame tg@slartibartfast:~/uni/datasets/nk/xds_run3$ identify DX-CORRECTIONS.tiff DX-CORRECTIONS.tiff TIFF 768x768 768x768+0+0 8-bit PseudoClass 256c 592KB 0.000u 0:00.000 Cheers, Tim On 01/10/2013 09:59 PM, Frank von Delft wrote: Brilliant - thanks Nat!! Easy to work around that feature. And thanks Nick!! Original Message Subject: Re: [ccp4bb] Convert cbf to png/tiff? Date: Thu, 10 Jan 2013 12:47:21 -0800 From: Nat Echols nathaniel.ech...@gmail.com To: Frank von Delft frank.vonde...@sgc.ox.ac.uk Using any recent Phenix distribution: labelit.png file_name For reasons unknown to me, the output is named plain.png - I will bug Nick about this. On Thu, Jan 10, 2013 at 12:36 PM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: Hello all - anybody know an easy way to convert CBF images (Pilatus) into something lossless like tiff or png? Ideally *easy* as in r e a l l y e a s y and not requiring extensive installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQ8FE+UxlJ7aRr7hoRApmAAKCNjwmHe8q5QpoFA9V3cSVtMwLqbgCgxwIa xwICsaEtz3Phoe6uM2kJ308= =fdKq -END PGP SIGNATURE-
Re: [ccp4bb] Fwd: Re: [ccp4bb] Convert cbf to png/tiff?
Normally the input files for Labelit must have sequential numbering like lysozyme_001.cbf. The file name DX-CORRECTIONS.cbf causes the reported error as it does not conform to this format. Nick On Fri, Jan 11, 2013 at 9:51 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 The formatting of icedove probably created confusion, but these error message come from running labelit.png WITH the file DX-CORRECTIONS.cbf as one and only command line option and no output is created. adxv has not problem dealing with XDS cbf-files. Tim On 01/11/2013 06:43 PM, Nat Echols wrote: I think the help message refers to another program. Anyway, it's an extremely simple script - having examined the code, the command-line invocation is: labelit.png input_file [output_file] and that's it - no other options available. But Nick or I will fix it so it prints something more useful if run without arguments. -Nat On Fri, Jan 11, 2013 at 9:33 AM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: I got that error blurb too when I run without an image on the commandline. Not very elegant. Try: labelit.png --help On 11/01/2013 16:34, Tim Gruene wrote: Hi Nat! How recent is recent? From today's 'phenix-online.org': New Phenix version 1.8.1 now available, but tg@slartibartfast:~/uni/datasets/nk/xds_run3$ labelit.png_1.8.1-1168 DX-CORRECTIONS.cbf Traceback (most recent call last): File /xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py, line 27, in module OV = overlay_plain(infile,graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/../../labelit/command_line/png.py, line 6, in __init__ OverlayDriverClass.__init__(self,infile,graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/overlay_distl.py, line 19, in __init__ self.I = GenericImageWorker(infile,binning=graphics_bin) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/graphics/support.py, line 12, in __init__ images = ImageFiles(imagenames,labelit_commands) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py, line 184, in __init__ self.filenames = FileNames(arg_module,phil_params) File /xtal/Suites/Phenix/phenix-1.8.1-1168/labelit/command_line/imagefiles.py, line 70, in __init__ self.interface3_parse_command() File /xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py, line 138, in interface3_parse_command self.interface3_FN_factory(os.path.abspath(file),error_message=File name not accepted) File /xtal/Suites/Phenix/phenix-1.8.1-1168/cctbx_project/spotfinder/diffraction/imagefiles.py, line 127, in interface3_FN_factory raise Exception(Input error: +error_message) Exception: Input error: File name not accepted Compared to: tg@slartibartfast:~/uni/datasets/nk/xds_run3$ adxv -sa DX-CORRECTIONS.cbf DX-CORRECTIONS.tiff Adxv Version 1.9.8 Copyright (C) 1994-2011 by Andrew Arvai, Area Detector Systems Corporation Recognized CBF format data. Warning: Could not find diffrn_frame_data or diffrn_data_frame tg@slartibartfast:~/uni/datasets/nk/xds_run3$ identify DX-CORRECTIONS.tiff DX-CORRECTIONS.tiff TIFF 768x768 768x768+0+0 8-bit PseudoClass 256c 592KB 0.000u 0:00.000 Cheers, Tim On 01/10/2013 09:59 PM, Frank von Delft wrote: Brilliant - thanks Nat!! Easy to work around that feature. And thanks Nick!! Original Message Subject: Re: [ccp4bb] Convert cbf to png/tiff? Date: Thu, 10 Jan 2013 12:47:21 -0800 From: Nat Echols nathaniel.ech...@gmail.com To: Frank von Delft frank.vonde...@sgc.ox.ac.uk Using any recent Phenix distribution: labelit.png file_name For reasons unknown to me, the output is named plain.png - I will bug Nick about this. On Thu, Jan 10, 2013 at 12:36 PM, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote: Hello all - anybody know an easy way to convert CBF images (Pilatus) into something lossless like tiff or png? Ideally *easy* as in r e a l l y e a s y and not requiring extensive installation of dependencies and stuff. Because then I might as well write my own stuff using cbflib and PIL in python. Thanks! phx -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQ8FE+UxlJ7aRr7hoRApmAAKCNjwmHe8q5QpoFA9V3cSVtMwLqbgCgxwIa xwICsaEtz3Phoe6uM2kJ308= =fdKq -END PGP SIGNATURE- -- Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Physical Biosciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA
[ccp4bb] Junior research position in Structural Biology
***NB: Posted on behalf of Dr. Macedo-Ribeiro, whom you should contact for further information (e-mail address below).*** The Associate Laboratory IBMC-INEB is recruiting a highly motivated researcher to integrate a multidisciplinary team in the field of the Biochemistry and Structural Biology of enzymes associated with human diseases. A PhD in the appropriate disciplines is mandatory. Previous post-doctoral research experience and demonstrated skills in Biochemistry and Structural Biology are required. Contract: The fixed term contract is limited to 28 months and expected to begin on March 1st 2013. The monthly gross salary amounts to 3.191,82 Euros. Job description: The regulation of biological and pathological processes is achievable through specific inhibition, spatial and temporal compartmentalization, and post-translational modification of the intervening enzymes. Impairment of any of these regulative mechanisms often results in serious pathologies to which specific therapeutic approaches can be conceived by understanding the molecular details of enzyme specificity, as well as of their strict regulation. In order to address the role played by macromolecular interactions and/or regulation by post-translational modifications in enzyme activity and specificity, we use protein X-ray crystallography along with a plethora of complementary biophysical/biochemical techniques. We are especially interested in elucidating the molecular mechanisms of action of proteins associated with neurodegenerative and infectious diseases ( http://www.ibmc.up.pt/research/research-groups/protein-crystallography). Application deadline: 20/01/2013 All details required for application can be found at: http://www.eracareers.pt/opportunities/index.aspx?task=globaljobId=32498 Applications must be submitted online: http://www.ibmc.up.pt/institute/open-positions (position Ciência 2008 Substituição--CONT_DOUT/23/IBMC/316/10253/17/2008). For more information please contact: Dr. Sandra Macedo-Ribeiro Protein Crystallography Group IBMC- Instituto de Biologia Molecular e Celular Rua do Campo Alegre, 823 4150-180 Porto, Portugal (sribeiro_at_ibmc.up.pt) -- Pedro J. B. Pereira, PhD IBMC - Biomolecular Structure Group Rua do Campo Alegre, 823 4150-180 Porto Portugal Tel. +351 226 074 900 Fax +351 226 099 157
[ccp4bb] a challenge
I have a challenge for all those expert model-builders out there: can you beat the machine? It seems these days that everything is automated, and the only decision left for a crystallographer to make is which automation package to use. But has crystallography really been solved? Is looking at maps now no more interesting than playing chess, or any of the other once noble pursuits of human beings that we no longer see as challenging because someone built a machine that can do the job better than any of us? I think not. But I need your help to prove it. Specifically, the phases in this file: http://bl831.als.lbl.gov/~jamesh/challenge/possible.mtz when fed with the right set of parameters into the best model building package I have available to me actually does converge to the correct structure, with nice low R/Rfree. However, THIS file: http://bl831.als.lbl.gov/~jamesh/challenge/impossible.mtz contains the same amplitudes but very slightly different phases from those in possible.mtz above, and this file invariably leads to abysmal failure of every model-building package I have tried. Short of cheating (aka using molecular replacement with the right ansswer: 3dko), I don't think there is any automated way to arrive at a solved structure from impossible.mtz. What is interesting about this is how remarkably similar these two maps are. In fact, the correlation coefficient between them is 0.92. And yet, one can be solved automatically, and the other can't. More details can be found on the web page: http://bl831.als.lbl.gov/~jamesh/challenge/ But, my question for the CCP4BB is: Are there any John Henrys left out there who can still beat the machine? Anyone? -James Holton MAD Scientist
[ccp4bb] CCP4 Update 013
Dear CCP4 Users, A CCP4 update has just been released, consisting of the following changes: All systems: * molrep: Significantly more accurate packing function implemented * pisa: Now reports on monomeric properties ina no-complex situations * JLigand: Compounds derived from smile strings are now automatically regularised * QtRView: Improved performance on large log files, added inverse resolution scale in graphs, coot and ccp4mg configuration is now optionally imported from ccp4i settings Linux only: * Ensembler and Sculptor: Fixed file permissions in order to enable users other than root to use these applications Windows only: * Crank: Fix for preventing terminal windows from popping up * CProdrg: HETATM notations synchronized with Refmac * Pointless and Aimless: Now able to handle twice bigger datasets * Scala: Corrections to plot titles * Phaser: Added missing cctbx library files If you do not currently receive updates, consider re-installing your CCP4 setup using the latest binary packages, which now have CCP4 Update manager (ccp4um) integrated. Note that auto-updates will work correctly only with CCP4 release 6.3.0, therefore upgrade if necessary. Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk Many thanks for using CCP4. Eugene Krissinel -- Scanned by iCritical.
Re: [ccp4bb] a challenge
Hi James, As an aside (as your point is looking for a John Henry, not investigating automated model-building) I would point out that it is not uncommon at all to find cases where a very small difference in starting parameters or starting phases leads to a very different final result in automated model-building. I suspect that this comes from the discrete nature of model-building: an atom goes either here or there and every time you put in something you have branched the search...then when this model is used in calculating a map you get a new map that depends on the exact branching...so that small starting perturbations can become amplified. As you have found a way to automatically build possible.mtz I would expect that some small change in parameters or software would solve the impossible one too (not that one could necessarily find this change easily). All the best, Tom T On Jan 11, 2013, at 12:13 PM, James Holton wrote: I have a challenge for all those expert model-builders out there: can you beat the machine? It seems these days that everything is automated, and the only decision left for a crystallographer to make is which automation package to use. But has crystallography really been solved? Is looking at maps now no more interesting than playing chess, or any of the other once noble pursuits of human beings that we no longer see as challenging because someone built a machine that can do the job better than any of us? I think not. But I need your help to prove it. Specifically, the phases in this file: http://bl831.als.lbl.gov/~jamesh/challenge/possible.mtz when fed with the right set of parameters into the best model building package I have available to me actually does converge to the correct structure, with nice low R/Rfree. However, THIS file: http://bl831.als.lbl.gov/~jamesh/challenge/impossible.mtz contains the same amplitudes but very slightly different phases from those in possible.mtz above, and this file invariably leads to abysmal failure of every model-building package I have tried. Short of cheating (aka using molecular replacement with the right ansswer: 3dko), I don't think there is any automated way to arrive at a solved structure from impossible.mtz. What is interesting about this is how remarkably similar these two maps are. In fact, the correlation coefficient between them is 0.92. And yet, one can be solved automatically, and the other can't. More details can be found on the web page: http://bl831.als.lbl.gov/~jamesh/challenge/ But, my question for the CCP4BB is: Are there any John Henrys left out there who can still beat the machine? Anyone? -James Holton MAD Scientist
